Messenger RNA conformations in the ribosomal E site revealed by X-ray crystallography

Abstract

A comparison of messenger RNA in X-ray crystal structures of 70S ribosomal complexes in the initiation, post-initiation and elongation states of translation shows distinct conformational differences in the exit (E) codon. Here, we present structural evidence indicating that, after the initiation event, the E codon nucleotides relax and form a classical A-helical conformation. This conformation is similar to that of the P and A codons, and is favourable for establishing Watson-Crick interactions with the anticodon of E-site transfer RNA.

Figure 1

Codon–anticodon interaction in the E site. (A,B) Structure of E, P and A codons in initiation (A) and post-initiation complexes (B). Sequences of the messenger RNA (mRNA) and the Shine–Dalgarno (SD) duplex (in red) are also shown. (C,D) E-site tRNA interaction with the E anticodon in initiation (C) and post-initiation (D) complexes. The E codon can adopt the classical A-helical conformation that enables base pairing with the anticodon of E-site tRNA only in the post-initiation complex. (E) Fourier (F_o−F_c) electron density map calculated at a resolution of 5.5 Å with E-site tRNA and mRNA omitted from the model. E site, exit site.

Figure 2

A detailed view of the ribosomal environment of the E codon in the post-initiation complex. Nucleotides directly involved in the stabilization of the E codon triplet structure are shown as yellow spheres. The residues of the S7 β-hairpin (shown as green spheres) are not in direct contact with the E codon, but are instead interacting with the upstream bases. E, exit site; h, helix; mRNA, messenger RNA; tRNA, transfer RNA.